Way Elite solar charger/controller malfunction

That’s great to hear.  IMO they are only fixing half your problems. 
solar controller crapped out. No big deal. Easy replacement. 
battery dead.  Great they are replacing it but first it “should” have lasted longer if it’s actually a bad battery. But entirely possible it’s just a defective battery that won’t charge. 
However you suspect a parasitic draw and that literally takes 2 min to diagnose. 
If that the case, that is the most important thing the dealer needs to fix. And assuming you better get it now while they’re being generous about goodwill warranty. A battery and cheap charge controller are just parts replacing. 
I’d diagnose the presence of a draw before even taking it in, so you can be confident in what they need to fix. 
No, it shouldn’t go dead in 2 weeks. Or 2 months.  Maintainer shouldn’t be mandatory for a couple months in nice weather. 

to bad they wouldn't let you pick the brand, If you have the choice out of thoes two I would go with the go power, even though I wouldn't recomend them to some one spending their own money.  not the same company they were when they were Canadian owned.

It's a Way Elite - which is apparently out of business stemming from a lot of problems according to other forums. Yes, I need to replace it. That's really the crux of my question, with what?

FR is looking into a good faith replacement under warranty (I am a few months out of my factory warranty). If they don't cover it then yes, I need to replace it myself. Doesn't need to be expensive or complicated. The controller is really only for a trickle charge to keep the batts topped off in storage. I have one 100w panel, and 1 house batt and one chassis battery. (Technically I have 2 house batts in parallel, but the controller sees it as one).  Based on that I really only need a 20A controller with slots for dual battery and I would like a separate readout panel - if anything to ensure it's working and cover the existing hole for the readout panel on the one I have now. Most have a readout on the controller itself, which is kind of silly since it's buried under the cabinets where you'll never be able to read it. I don't know much about controllers but from what I am learning, they are all pretty much the same with some being better quality than others. Ones for dual batteries seem to be harder to find, and ones with a separate readout panel even harder. And like I said, I don't know good from bad.  

So, any recommendations for a controller with a remote readout for a 100W panel, and 2 batts. 

So, examining it more closely, the "burnt" sections are in each place where the heat shrink tubing was put over the connection and it looks like they got a little happy with the torch. It's a little scorched on the wire insulation - outside rather than coming from the wire itself. Fuses are good, so I think I can rule out a short. After I posted this, I called my Dealer and FR. Both of which I have been very happy with so far and my second FR product purchased from them. It's only just out of warranty so the FR rep said he can probably get a good faith replacement for me and he'll get back to me. On the off chance they can't/won't I'll still need a recommendation on an aftermarket charger/controller. Seems they run anywhere from $50-$200 and I wouldn't know a good one from Shinola.